Intelligent Design Investigation

Research Sources

Molecular Machines and Integrated Biological Systems  •  26 unique sources
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These are the research sources used in this investigation. A source is listed once even when it supports several evidence records, explanations, or objections. The entries below also show where each source is used so that the research trail can be followed.

Yildiz et al. — Kinesin Walks Hand-Over-Hand

Author: Ahmet Yildiz; Michio Tomishige; Ronald D. Vale; Paul R. Selvin
Kinesin Walks Hand-Over-Hand • Science • 2004
Scientific Research Neutral
DOI: 10.1126/science.1093753
Used in this investigation
Evidence
  • Kinesin, Dynein, and Intracellular Transport — Experimental Evidence

Barabási and Oltvai — Network Biology and Cellular Organization

Author: Albert-László Barabási; Zoltán N. Oltvai
Network Biology: Understanding the Cell's Functional Organization • Nature Reviews Genetics • 2004
Scientific Review Neutral
DOI: 10.1038/nrg1272
Used in this investigation
Evidence
  • Integrated Cellular Systems — Network Organization
Explanations
  • Integrated Cellular Organization — Network Organization

Horwich et al. — Chaperonin Physiology and Mechanism

Author: Arthur L. Horwich; Wayne A. Fenton; Eli Chapman; George W. Farr
Two Families of Chaperonin: Physiology and Mechanism • Annual Review of Cell and Developmental Biology • 2007
Scientific Review Neutral
DOI: 10.1146/annurev.cellbio.23.090506.123555
Used in this investigation
Evidence
  • Protein Folding and Molecular Chaperones — Chaperone Mechanism

Alberts — The Cell as a Collection of Protein Machines

Author: Bruce Alberts
The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists • Cell • 1998
Scientific Review Neutral
DOI: 10.1016/S0092-8674(00)80922-8
Used in this investigation
Evidence
  • Molecular Machines in the Cell — Scientific Foundation
  • Integrated Cellular Systems — Scientific Foundation
Explanations
  • Molecular Machines as Functional Systems — Scientific Foundation
  • Integrated Cellular Organization — System Integration
Questions & Objections
  • Is "Molecular Machine" Only an Analogy? — Scientific Terminology

Anfinsen — Principles Governing Protein Folding

Author: Christian B. Anfinsen
Principles That Govern the Folding of Protein Chains • Science • 1973
Scientific Research Neutral
DOI: 10.1126/science.181.4096.223
Used in this investigation
Evidence
  • Protein Folding and Molecular Chaperones — Scientific Foundation

Finley — Recognition and Processing by the Proteasome

Author: Daniel Finley
Recognition and Processing of Ubiquitin-Protein Conjugates by the Proteasome • Annual Review of Biochemistry • 2009
Scientific Review Neutral
DOI: 10.1146/annurev.biochem.78.081507.101607
Used in this investigation
Evidence
  • Protein Degradation and the Proteasome — Scientific Foundation

Hartl et al. — Molecular Chaperones and Proteostasis

Author: F. Ulrich Hartl; Andreas Bracher; Manajit Hayer-Hartl
Molecular Chaperones in Protein Folding and Proteostasis • Nature • 2011
Scientific Review Neutral
DOI: 10.1038/nature10317
Used in this investigation
Evidence
  • Protein Folding and Molecular Chaperones — System Integration

Chevance and Hughes — Coordinating Flagellar Assembly

Author: Fabienne F. V. Chevance; Kelly T. Hughes
Coordinating Assembly of a Bacterial Macromolecular Machine • Nature Reviews Microbiology • 2008
Scientific Review Neutral
DOI: 10.1038/nrmicro1887
Used in this investigation
Evidence
  • Molecular Machines in the Cell — Specific Example
  • The Bacterial Flagellum — Scientific Foundation
  • Assembly of the Bacterial Flagellum — Scientific Foundation

Noller et al. — Ribosome Mechanics and Translocation

Author: Harry F. Noller; Laura Lancaster; Jie Zhou; Srividya Mohan
The Ribosome Moves: RNA Mechanics and Translocation • Nature Structural & Molecular Biology • 2017
Scientific Review Neutral
DOI: 10.1038/nsmb.3505
Used in this investigation
Evidence
  • The Ribosome as a Molecular Machine — Mechanical Translocation

Noji et al. — Direct Observation of F1-ATPase Rotation

Author: Hiroyuki Noji; Ryohei Yasuda; Masasuke Yoshida; Kazuhiko Kinosita Jr.
Direct Observation of the Rotation of F1-ATPase • Nature • 1997
Scientific Research Neutral
DOI: 10.1038/386299a0
Used in this investigation
Evidence
  • ATP Synthase: A Rotary Molecular Motor — Experimental Evidence
Explanations
  • Molecular Machines as Functional Systems — Experimental Evidence
Questions & Objections
  • Is "Molecular Machine" Only an Analogy? — Experimental Function

Abrahams et al. — Structure of F1-ATPase

Author: Jan Pieter Abrahams; Andrew G. W. Leslie; René Lutter; John E. Walker
Structure at 2.8 Å Resolution of F1-ATPase from Bovine Heart Mitochondria • Nature • 1994
Scientific Research Neutral
DOI: 10.1038/370621a0
Used in this investigation
Evidence
  • ATP Synthase: A Rotary Molecular Motor — Structural Context

Bard et al. — Structure and Function of the 26S Proteasome

Author: Jared A. M. Bard; Ellen A. Goodall; Eric R. Greene; Erik Jonsson; Ken C. Dong; Andreas Martin
Structure and Function of the 26S Proteasome • Annual Review of Biochemistry • 2018
Scientific Review Neutral
DOI: 10.1146/annurev-biochem-062917-011931
Used in this investigation
Evidence
  • Protein Degradation and the Proteasome — Degradation Mechanism

True and Carroll — Gene Co-Option in Evolution

Author: John R. True; Sean B. Carroll
Gene Co-Option in Physiological and Morphological Evolution • Annual Review of Cell and Developmental Biology • 2002
Scientific Review Supports Evolutionary Explanation
DOI: 10.1146/annurev.cellbio.18.020402.140619
Used in this investigation
Evidence
  • Co-option and Evolutionary Pathways — Scientific Foundation
Explanations
  • Evolution by Modification and Co-option — Co Option
Questions & Objections
  • Can Co-option Build Complex Molecular Systems? — Co Option
  • Does Irreducible Complexity Really Prevent Evolution? — Co Option

Hartwell et al. — From Molecular to Modular Cell Biology

Author: Leland H. Hartwell; John J. Hopfield; Stanislas Leibler; Andrew W. Murray
From Molecular to Modular Cell Biology • Nature • 1999
Scientific Review Neutral
DOI: 10.1038/35011540
Used in this investigation
Evidence
  • Integrated Cellular Systems — Functional Integration
Explanations
  • Integrated Cellular Organization — Functional Modules

Pallen and Matzke — Evolutionary Origin of Bacterial Flagella

Author: Mark J. Pallen; Nicholas J. Matzke
From The Origin of Species to the Origin of Bacterial Flagella • Nature Reviews Microbiology • 2006
Scientific Review Supports Evolutionary Explanation
DOI: 10.1038/nrmicro1493
Used in this investigation
Evidence
  • Irreducible Complexity — Evolutionary Response
  • Can Molecular Machines Be Built Step by Step? — Evolutionary Response
Explanations
  • Irreducible Complexity and the Design Argument — Evolutionary Response
Questions & Objections
  • Does Irreducible Complexity Really Prevent Evolution? — Evolutionary Response
  • Does the Bacterial Flagellum Have an Evolutionary History? — Evolutionary Model
  • Is Design Just Filling Gaps in Evolutionary Knowledge? — Evolutionary Response

Pallen and Gophna — Flagella, Type III Secretion, and Evolution of Complexity

Author: Mark J. Pallen; Uri Gophna
Bacterial Flagella and Type III Secretion: Case Studies in the Evolution of Complexity • Genome Dynamics • 2007
Scientific Review Supports Evolutionary Explanation
DOI: 10.1159/000107602
Used in this investigation
Evidence
  • Irreducible Complexity — Evolutionary Mechanisms
  • Co-option and Evolutionary Pathways — Evolutionary Mechanisms
Explanations
  • Evolution by Modification and Co-option — Comparative Evidence
Questions & Objections
  • Can Co-option Build Complex Molecular Systems? — System Relationships
  • Does Homology Explain the Origin of Molecular Machines? — System Homology

Behe — Darwin's Black Box and Irreducible Complexity

Author: Michael J. Behe
Darwin's Black Box: The Biochemical Challenge to Evolution • Free Press • 1996
Book Supports Design
Used in this investigation
Evidence
  • Irreducible Complexity — Design Argument
  • Can Molecular Machines Be Built Step by Step? — Design Argument
Explanations
  • Irreducible Complexity and the Design Argument — Design Argument
  • Can Molecular Machines Be Built Step by Step? — Design Challenge
Questions & Objections
  • Does Irreducible Complexity Really Prevent Evolution? — Design Argument
  • Is Design Just Filling Gaps in Evolutionary Knowledge? — Design Argument

Nissen et al. — Structural Basis of Peptide Bond Synthesis

Author: Poul Nissen; Jeffrey Hansen; Nenad Ban; Peter B. Moore; Thomas A. Steitz
The Structural Basis of Ribosome Activity in Peptide Bond Synthesis • Science • 2000
Scientific Research Neutral
DOI: 10.1126/science.289.5481.920
Used in this investigation
Evidence
  • The Ribosome as a Molecular Machine — Catalytic Mechanism

Liu and Ochman — Stepwise Formation of the Bacterial Flagellar System

Author: Renyi Liu; Howard Ochman
Stepwise Formation of the Bacterial Flagellar System • Proceedings of the National Academy of Sciences • 2007
Scientific Research Supports Evolutionary Explanation
DOI: 10.1073/pnas.0700266104
Used in this investigation
Evidence
  • Can Molecular Machines Be Built Step by Step? — Evolutionary Reconstruction
Explanations
  • Irreducible Complexity and the Design Argument — Stepwise Reconstruction
  • Can Molecular Machines Be Built Step by Step? — Evolutionary Reconstruction
Questions & Objections
  • Does the Bacterial Flagellum Have an Evolutionary History? — Stepwise Reconstruction
  • Does Homology Explain the Origin of Molecular Machines? — Gene Homology
  • Is Design Just Filling Gaps in Evolutionary Knowledge? — Empirical Reconstruction

Tomko and Hochstrasser — Architecture and Assembly of the Proteasome

Author: Robert J. Tomko Jr.; Mark Hochstrasser
Molecular Architecture and Assembly of the Eukaryotic Proteasome • Annual Review of Biochemistry • 2013
Scientific Review Neutral
DOI: 10.1146/annurev-biochem-060410-150257
Used in this investigation
Evidence
  • Protein Degradation and the Proteasome — System Architecture

Macnab — How Bacteria Assemble Flagella

Author: Robert M. Macnab
How Bacteria Assemble Flagella • Annual Review of Microbiology • 2003
Scientific Review Neutral
DOI: 10.1146/annurev.micro.57.030502.090832
Used in this investigation
Evidence
  • The Bacterial Flagellum — Structural Context
  • Assembly of the Bacterial Flagellum — Assembly Mechanism

Vale — The Molecular Motor Toolbox for Intracellular Transport

Author: Ronald D. Vale
The Molecular Motor Toolbox for Intracellular Transport • Cell • 2003
Scientific Review Neutral
DOI: 10.1016/S0092-8674(03)00111-9
Used in this investigation
Evidence
  • Kinesin, Dynein, and Intracellular Transport — Scientific Foundation

Reck-Peterson et al. — Cytoplasmic Dynein Transport Machinery

Author: Samara L. Reck-Peterson; William B. Redwine; Ronald D. Vale; Andrew P. Carter
The Cytoplasmic Dynein Transport Machinery and Its Many Cargoes • Nature Reviews Molecular Cell Biology • 2018
Scientific Review Neutral
DOI: 10.1038/s41580-018-0004-3
Used in this investigation
Evidence
  • Kinesin, Dynein, and Intracellular Transport — System Integration

Abby and Rocha — Evolution of Type III Secretion from the Flagellum

Author: Sophie S. Abby; Eduardo P. C. Rocha
The Non-Flagellar Type III Secretion System Evolved from the Bacterial Flagellum and Diversified into Host-Cell Adapted Systems • PLoS Genetics • 2012
Scientific Research Supports Evolutionary Explanation
DOI: 10.1371/journal.pgen.1002983
Used in this investigation
Evidence
  • Co-option and Evolutionary Pathways — Comparative Evidence
  • Can Molecular Machines Be Built Step by Step? — Comparative Evidence
Explanations
  • Evolution by Modification and Co-option — Evolutionary Reconstruction
  • Can Molecular Machines Be Built Step by Step? — Comparative Evidence
Questions & Objections
  • Can Co-option Build Complex Molecular Systems? — Evolutionary Reconstruction
  • Does the Bacterial Flagellum Have an Evolutionary History? — Comparative Genomics
  • Does Homology Explain the Origin of Molecular Machines? — Phylogenetic Reconstruction

Ramakrishnan — Ribosome Structure and the Mechanism of Translation

Author: Venkatraman Ramakrishnan
Ribosome Structure and the Mechanism of Translation • Cell • 2002
Scientific Review Neutral
DOI: 10.1016/S0092-8674(02)00619-0
Used in this investigation
Evidence
  • The Ribosome as a Molecular Machine — Scientific Foundation
Explanations
  • Molecular Machines as Functional Systems — Information Processing
Questions & Objections
  • Is "Molecular Machine" Only an Analogy? — Molecular Structure

Kühlbrandt — Structure and Mechanisms of F-Type ATP Synthases

Author: Werner Kühlbrandt
Structure and Mechanisms of F-Type ATP Synthases • Annual Review of Biochemistry • 2019
Scientific Review Neutral
DOI: 10.1146/annurev-biochem-013118-110903
Used in this investigation
Evidence
  • ATP Synthase: A Rotary Molecular Motor — Scientific Foundation
 Sources are gathered from the evidence, explanations, and objections linked to this investigation and are shown once per source.